class MirandaHit(object):
""" Object oriented class containing informations of one miranda hit """
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
#~~~~~~~CLASS FIELDS~~~~~~~#
ID_COUNT = 0
#~~~~~~~CLASS METHODS~~~~~~~#
@ classmethod
def next_id (self):
cur_id = self.ID_COUNT
self.ID_COUNT +=1
return cur_id
#~~~~~~~FONDAMENTAL METHODS~~~~~~~#
def __init__(self, q_id, s_id, score, energy, q_start, q_end, s_start, s_end, length, identity, homology):
""" Create a MirandaHit object """
# Store parameters in self variables
self.id = self.next_id()
self.q_id = q_id
self.s_id = s_id
self.score = float(score)
self.energy = float(energy)
self.q_start = int(q_start)
self.q_end = int(q_end)
self.s_start = int(s_start)
self.s_end = int(s_end)
self.length = int(length)
self.identity = float(identity[:-1])
self.homology = float(homology[:-1])
# Parse the gff_line in the contained in the subject id
self.gff = GffLine(self.s_id)
def __str__(self):
msg = "HIT {}".format(self.id)
msg += "\tQuery\t{}:{}-{}\n".format(self.q_id, self.q_start, self.q_end)
msg += "\tSubject\t{}:{}-{}\n".format(self.s_id, self.s_start, self.s_end)
msg += "\tLenght : {}\tIdentity : {}%\Homology : {}%\tScore : {}\tEnergy : {}\n".format(
self.length, self.identity, self.homology, self.score, self.energy )
return (msg)
def __repr__(self):
return "<Instance of {} from {} >\n".format(self.__class__.__name__, self.__module__)
def report (self):
"""Return and ordered dict containing all the required informations"""
report = OrderedDict()
for key, val in self.gff.report().items():
report ["subject_"+key] = val
report ["subject_hit_start"] = self.s_start+1
report ["subject_hit_end"] = self.s_end
report ["query"] = self.q_id
report ["query_hit_start"] = self.q_start+1
report ["query_hit_end"] = self.q_end
report ["hit_score"] = self.score
report ["hit_energy"] = self.energy
report ["hit_length"] = self.length
report ["hit_identity"] = self.identity
report ["hit_homology"] = self.homology
return report
class BlastHit(object):
""" Object oriented class containing informations of one blast hit """
# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~#
# ~~~~~~~CLASS FIELDS~~~~~~~#
ID_COUNT = 0
# ~~~~~~~CLASS METHODS~~~~~~~#
@classmethod
def next_id(self):
cur_id = self.ID_COUNT
self.ID_COUNT += 1
return cur_id
# ~~~~~~~FONDAMENTAL METHODS~~~~~~~#
def __init__(self, q_id, s_id, identity, length, mis, gap, q_start, q_end, s_start, s_end, evalue, score, q_seq):
""" Create a BlastHit object """
# Store parameters in self variables
self.id = self.next_id()
self.q_id = q_id
self.s_id = s_id
self.identity = float(identity)
self.length = int(length)
self.mis = int(mis)
self.gap = int(gap)
self.evalue = float(evalue)
self.score = float(score)
self.q_seq = q_seq
self.q_start = int(q_start) - 1
self.q_end = int(q_end)
# Parse the gff_line in the contained in the subject id
self.gff = GffLine(self.s_id)
# Correct coordinates of hit for python 0 based coordinates depending of the orientation
if int(s_start) < int(s_end):
self.strand = "+"
self.s_start = int(s_start) - 1
self.s_end = int(s_end)
else:
self.strand = "-"
self.s_start = int(s_end) - 1
self.s_end = int(s_start)
def __str__(self):
msg = "HIT {}".format(self.id)
msg += "\tQuery\t{}:{}-{}({})\n".format(self.q_id, self.q_start, self.q_end)
msg += "\tSubject\t{}:{}-{}({})\n".format(self.s_id, self.s_start, self.s_end, self.strand)
msg += "\tLenght : {}\tIdentity : {}%\tEvalue : {}\tBit score : {}\n".format(
self.length, self.identity, self.evalue, self.score
)
msg += "\tAligned query seq : {}\n".format(self.q_seq)
return msg
def __repr__(self):
return "<Instance of {} from {} >\n".format(self.__class__.__name__, self.__module__)
def report(self):
"""Return and ordered dict containing all the required informations"""
report = OrderedDict()
for key, val in self.gff.report().items():
report["subject_" + key] = val
report["subject_hit_start"] = self.s_start + 1
report["subject_hit_end"] = self.s_end
report["query"] = self.q_id
report["query_hit_start"] = self.q_start + 1
report["query_hit_end"] = self.q_end
report["hit_score"] = self.score
report["hit_evalue"] = self.evalue
report["hit_length"] = self.length
report["hit_identity"] = self.identity
report["hit_gap"] = self.gap
report["hit_mismatch"] = self.mis
return report